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Curriculum Vitae, January 2017 Lior Pachter Bren Professor of Computational Biology Departments of Biology and Phone: (510) 664-4847 Computing & Mathematical Sciences Fax: (510) 642-8204 California Institute of Technology [email protected] Pasadena, CA 94720-3840, USA http://pachterlab.github.io/ Positions Held California Institute of Technology (1/17{present) ◦ Bren Professor of Computational Biology Departments of Biology and Computing & Mathematical Sciences University of California, Berkeley (8/99{present) ◦ Raymond and Beverly Sackler Chair in Computational Biology (7/12{present) ◦ Director, Center for Computational Biology (1/10{6/13) ◦ Professor of Mathematics, Molecular & Cell Biology and Computer Science (7/09{present) Member, Graduate Groups in Computational Biology, Biostatistics, Computational Science and Engineering and the Joint UCSF/Berkeley Program in Bioengineering Member, QB3 California Institute for Quantitative Biomedical Research Member, Synthetic Biology Institute Affiliate, Simons Institute for Theory of Computing ◦ Associate Professor of Mathematics, Molecular & Cell Biology and Computer Science (7/08{7/09) ◦ Associate Professor of Mathematics & Computer Science (7/06{7/08) ◦ Associate Professor of Mathematics (7/05{7/06) ◦ Assistant Professor of Mathematics (8/01{6/05) ◦ Visiting Assistant Professor of Mathematics (8/99{8/01) University of Oxford (9/06{07/07) ◦ Visiting Professor (while on sabbatical) Visitor, Mathematical Institute, hosted by Professor Philip K. Maini Visitor, Department of Statistics, hosted by Professor Jotun Hein 1 Lior Pachter Curriculum vitae, January 2017 Education Massachusetts Institute of Technology (9/94{6/99) ◦ PhD in Mathematics. Advisor: Professor Bonnie A. Berger Co-advisors Professor Eric S. Lander and Professor Daniel J. Kleitman. California Institute of Technology (9/90{6/94) ◦ B.S. in Mathematics. Caltech merit award for academic achievement. Honors, Awards and Fellowships ◦ Keynote Speaker: ISBCB (2014), ISMB (2013), FPSAC (2011) ◦ Bren Chair in Computational Biology (2017) ◦ Glenn Award (2013) ◦ Raymond and Beverly Sackler Chair in Computational Biology (2012) ◦ Cufflinks paper highlighted as a breakthrough of the year by Nat. Biotech. (2010). ◦ Miller Research Professorship (2009) ◦ Winner of best paper award for \multiple alignment by sequence annealing", (joint with Ariel Schwartz). 2006 European Conference on Computational Biology. ◦ NSF Faculty Early Career Development (CAREER) Award (2004). ◦ Sloan Research Fellow (2003{2004) computational and evolutionary molecular biology. ◦ Federal Laboratory Consortium for Technology Transfer Award (2003). Professional Activities ◦ Member, Board of Directors, Black Pine Circle School, 1/15{present. ◦ Member, Scientific Advisory Board, Maverix Biomics, 3/12{present. ◦ Member, Scientific Advisory Board, Mathematical Biosciences Institute, 11/08{12/11. ◦ Testimony as an expert witness (biotechnology and bioinformatics). 2 Lior Pachter Curriculum vitae, January 2017 Grants ◦ Algorithms and Software for Provably Accurate De Novo RNA-Seq Assembly, co-PI (with David Tse and Sreeram Kannan) 9/15{9/18 ($476,329), NIH (R01). ◦ Streaming algorithms for whole genome assembly, co-PI (with P´allMelsted) 1/15{12/15 (9,950,000 ISK = $83,000), Icelandic Research Fund. ◦ UCSC Center of Excellence for Big Data Computing in the Biomedical Sciences co-PI (Center PIs: David Haussler and David Patterson) 9/14{9/18 ($100,000), NIH (U54). ◦ Center for RNA Systems Biology co-PI computational core (Center PI: Jaimie Cate) 9/12{9/15 ($465,000 computational core), NIH (P50). ◦ Metagenome quantification using high-throughput sequencing, co-PI (with Kevin McLoughlin) 7/12{7/13 ($296,498), UC Lab Fees Research Program Award. ◦ Association mapping without genotyping, co-PI (with Michael Eisen) 4/12{4/15 ($406,120), NIH (R21). ◦ Agilent Research grant (funded through the Synthetic Biology Institute), PI 3/12{3/13 ($60,000). ◦ Erythroid stage-specific transcriptome expression, dynamics, and regulation, co-PI (with John Conboy) 9/11{5/16 ($2,380,104), NIH (R01). ◦ Methods for the analysis of RNA-Seq and related sequence census based experiments, PI 8/11{5/16 ($1,114,512), NIH (R01). ◦ Fundamental laws of biology, co-PI (with Bernd Sturmfels) 9/05{3/09 ($750,000), DARPA. ◦ CAREER: Comparison and Annotation of Multiple Whole Genomes, PI 6/04{6/09 ($400,000), NSF. ◦ GENCODE: The Encyclopedia of Genes and Gene Variants (main PI: Roderic Guig´o) 10/03{10/06 ($72,000), NIH. ◦ Cross-species gene finding and annotation, PI 6/02{6/05 ($928,728), NIH (R01). Fundraising ◦ Tata Consulting Services Research agreement with the Center for Computational Biology. 6/11{6/15 ($900,000 with additional $3 million in-kind contribution). ◦ David des Jardins (private donor) Funding for construction and support of the Laboratory for Mathematics and Computational Biology. 3/08{6/13 ($500,000) 3 Lior Pachter Curriculum vitae, January 2017 Publications Books 1. L. Pachter and B. Sturmfels: Algebraic Statistics for Computational Biology, Cam- bridge University Press, October 2005. Journal Publications 108. N. Bray, H. Pimentel, P. Melsted and L. Pachter, Near-optimal probabilistic RNA-Seq quantification, Nature Biotechnology, 34 (2016), p 525{527. 107. A. Mittal, L. Pachter, J.L. Nelson, H. Kjaergaard, M.K. Smed, V.L. Gildengorin, V. Zoffmann, M.L. Hetland, N.P. Jewell, J. Olsen and D. Jawaheer, Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheuma- toid Arthritis, PLoS One, (2015). 106. N.K. Hanchate, K. Kondoh, Z. Lu, D. Kuang, X. Ye, X. Qiu, L. Pachter, C. Trap- nell and L.B. Buck, Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis, Science, 350 (2015), p 1251{1255. 105. H. Pimentel, M. Parra, S. Gee, N. Mohandas, L. Pachter and J. Conboy, A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis, Nucleic Acids Research, 44 (2015), p 838{851. 104. D.J. Brat et al., Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas, New England Journal of Medicine, 372 (2015), p 2481{2498. 103. M. Singer and L. Pachter, Controlling for conservation in genome-wide DNA methyla- tion studies, BMC Genomics, 16 (2015), 420. 102. M. Singer, I. Kosti, L. Pachter and Y. Mandel-Gutfreund, Diverse epigenetic landscape at human exons with implication for expression, Nucleic Acids Research, 43 (2015), p 3498-3508. 101. S. Aviran and L. Pachter, Rational experimental design for sequencing-based RNA structure mapping, RNA, 20 (2014), p 1864{1877. 100. R. Forster, K. Chiba, L. Schaeffer, S.G. Regaldo, C.S. Lai, Q. Gao, S. Kiani, H.F. Farin, H. Clevers, G.J. Cost, A. Chan, E.J. Rebar, F.D. Urnov, P.D. Gregory, L. Pachter, R. Jaenisch and D. Hockemeyer, Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells, Stem Cell Reports, 2 (2014), p 838{852. 99. V.L. Wong, C.E. Ellison, M.B. Eisen, L. Pachter and R. Brem, Structural variation among wild and industrial strains of Penicillium chrysogenum, PLoS One, 9 (2014), e96784. 4 Lior Pachter Curriculum vitae, January 2017 98. S. Takayama, J. Dhahbi, A. Roberts, G. Mao, S.-J. Heo, L. Pachter, D.I.K. Martin and D. Boffelli, Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity, Genome Research, 24 (2014), p 821{830. 97. H. Pimentel, M. Parra, S. Gee, D. Ghanem, X. An, J. Li, N. Mohandas, L. Pachter and J. Conboy, A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis, Nucleic Acids Research, 42 (2014), p 4031{4042. 96. A. Roberts, H. Feng and L. Pachter, Fragment assignment in the cloud with eXpress-D, BMC Bioinformatics, 14 (2013), p 358. 95. A. Roberts, L. Schaeffer and L. Pachter, Updating RNA-Seq analyses after re-annotation, Bioinformatics, 29 (2013), p 1631{1637. 94. A. Rahman and L. Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14 (2013), R8. 93. C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, 31 (2013), p 46{53. 92. A. Roberts and L. Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods, 10 (2013), p 71{73. 91. S.A. Mortimer, C. Trapnell, S. Aviran, L. Pachter and J.B. Lucks, SHAPE-Seq: High throughput RNA structure analysis, Current Protocols in Chemical Biology, 4 (2012), p 275{297. 90. A. Kleinman, M. Harel and L. Pachter, Affine and projective tree metric theorems, Annals of Combinatorics, 17 (2012), p 205{228. 89. V. Hower, R. Starfield, A. Roberts, and L. Pachter, Quantifying uniformity in mapped reads, Bioinformatics, 28 (2012), 2680{2682. 88. L. Pachter, A closer look at RNA editing, Nature Biotechnology, 30 (2012), p 246{247. 87. C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn and L. Pachter, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (2012), p 562{ 578. 86. A. Roberts and L. Pachter, RNA-Seq and find: entering the RNA deep field, Genome Medicine, 3 (2011), p 74. 85. F. Meacham, D. Boffelli, J. Dhahbi, D.I.K. Martin, M. Singer and L. Pachter, Iden- tification and correction of systematic error in high-throughput sequence data, BMC Bioinformatics, 12 (2011), 451. 5 Lior Pachter Curriculum vitae, January 2017 84. M. Singer, A. Engstrom, A. Schoenhuth and L. Pachter, Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains, Sta- tistical Applications in Genetics and Molecular Biology, 10 (2011), Article 43. 83. D. Martin, M. Singer, J. Dhahbi, G. Mao, L. Zhang, G. Schroth, L. Pachter and D. Boffelli, Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states, Genome Research, 21 (2011), p 2049{2057. 82. A. Roberts, H. Pimentel, C. Trapnell and L. Pachter, Identification of novel transcripts in annotated genomes using RNA-Seq, Bioinformatics, 27 (2011), p 2325{2329.
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